Protein Structure and Folding Review

This flashcard set covers the introduction to protein structure, covering levels of organization from primary to quaternary, the mechanics of folding, and common motifs and domains.

Collagen

An example of a protein with a very linear shape.

Insulin

A small protein mentioned as having a specific functional shape.

Calmodulin

A protein with a dumbbell shape consisting of two globular domains connected by a linear region.

Peptide bond

A strong covalent bond that links the carboxyl group of one amino acid to the amino group of another; it is characterized as being rigid and planar.

N-terminus

The end of a peptide backbone that has an exposed amino group; also called the amino terminus.

C-terminus

The end of a peptide backbone that has an exposed carboxyl group; also called the carboxy terminus.

Primary structure

The simplest level of protein structure, referring to the specific sequence of amino acids.

Secondary structure

Structures that take place in a given part of a protein, primarily alpha helices and beta sheets, which make up about $60\%$ of a protein.

Random coil

A non-structured, intrinsically disordered region of a protein that joins structured regions and is often the site of modifications like phosphorylation.

Alpha helix

A spiral staircase-like secondary structure held together by hydrogen bonds between every first and fourth amino acid, completing a turn every $3.6$ amino acids.

Beta sheet

A secondary structure where parts of the peptide backbone are parallel or anti-parallel to each other, forming a pleated arrangement held by hydrogen bonds.

Prolysin and Glycine

Two specific amino acids that do not work well in an alpha helix because one kinks the backbone and the other has a side chain that is too small.

Motif

A subcategory under secondary structure that consists of a combination of secondary structures, such as an alpha helix and a beta sheet associated together.

Amphipathic alpha helix

A helix that has one side composed of polar amino acids and the other side composed of nonpolar amino acids.

Coiled-coil motif

A common motif formed by two alpha helices twisting together to hide hydrophobic side chains that form a candy cane-like stripe down the helix.

Tertiary structure

The overall three-dimensional folding of a whole protein, which often occurs in independent segments called domains.

Domain

A segment of a polypeptide chain that folds independently into a compact, stable structure, typically performing a unique function like catalysis or substrate binding.

Quaternary structure

The complex formed when separate proteins come together to accomplish a task, such as dimers, tetramers, or larger assemblies like a $60$-mer.

Macromolecular machine

A complex of many different proteins, and sometimes RNA, that come together to perform a cellular task, such as a ribosome.

Affinity

The ratio of the on-rate to the off-rate between two molecules; it describes the strength of their association based on non-covalent bonds.

Van der Waals attractions

The weakest non-covalent interactions, representing transient changes in atom charges when they get close to one another.

Oil drop model

A folding model where nonpolar side chains are buried on the inside of the protein to stay away from water, while polar side chains are on the surface.

Phi and Psi angles

The rotation angles around the alpha carbon in a peptide backbone; certain combinations are energetically favorable and lead to the formation of secondary structures.

Urea

A small molecule with high potential for hydrogen bonding that is used as a powerful protein denaturant.

Beta-mercaptoethanol

A powerful antioxidant used to break the covalent disulfide bonds formed between cysteine side chains.

Conservative substitution

Replacing one amino acid with another that has a similar size, shape, and charge, often resulting in only a subtle change to the protein's function.

Entropy

A measure of randomness or disorder; in protein folding, it is minimized as the protein reaches its highly ordered native structure.